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Overview of current practices in data analysis for wood identification. A guide for the different timber tracking methods.
Abstract and Figures
Today we have five types of timber tracking tools available. Each has its own strengths and limitations (see the Timber Tracking Tool Infogram), but together they offer a broad range of methods that can assist us in identifying the botanical as well as the geographic origin (provenance) of most kinds of timber samples, even those smaller than 1 cm³.
With this guide we want to provide an overview of the current best-practice methods used to analyse data derived from different wood identification methods, while presenting their respective strengths and limitations. We give advice on data analysis, from the development of reference data, through to the verification of identity and provenance of unknown samples against the reference database. We end with an expert view on combining methods for wood identification and discuss how timber identification possibilities could expand in the future.
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... Raw wood at any stage [3,57] The chemical methods, namely mass spectrometry, infrared spectroscopy, canine use, stable isotope analysis and the radiocarbon method are not applicable on their own for solid traceability. However, they are useful and cost-effective methods to randomly check the species, provenance and felling date [49]. ...
... Mass spectrometry is the collection of a set of molecules that create a chemical fingerprint that is verified with a database [49]. The most common is the ForeST Databank in the United States for the identification of economically important tree species. ...
... The comparison of the results is also done via a database. The creation of the database is complicated by the lack of standards of the equipment, the software, the settings and the nature of the samples in the procedure [49,53]. The method is particularly suitable for determining the moisture content of wood in the mill [54]. ...
Traceability is the ability to follow the processes that a raw material or product goes through. For forestry, this means identifying the wood from the standing tree to the mill entrance and recording all information about the technical (production) and spatial (transportation) manipulation of the timber by linking it to the ID. We reviewed the literature for developments in timber flow traceability. Findings range from disillusionment with the non-application of available forestry technology to enthusiasm for the advancement of technology that-given appropriate incentives of an economic, environmental, consumer-oriented and legislative nature-can rapidly lead to widespread end-to-end media-interruption-free implementation. Based on our research, the solution lies in optical biometric systems that identify the individual piece of wood-without attaching anything-at three crucial points: during assortment at the skid road, at the forest road and at the mill entrance. At all of these points, the data accruing during the timber supply process must be linked to the ID of the piece of wood via data management.
... www.nature.com/scientificreports/ near infrared spectroscopy) can provide more reliable forensic timber identification 8 . Each tool has its own strength and in combination they complement one another allowing authorities to overcome limitations of more traditional methods in species identification, geographic origin verification or linking illegal logs to the stumps of origin. ...
... Genetic approaches have been used to determine the origin of wood samples from many important species, including Neobalanocarpus heimii 9,10 , Gonystylus bancanus 11 , Acer macrophyllum 12 , Cedrela odorata 13 and Chamaecyparis taiwanensis 14 . To develop timber tracking tools suitable for these species, researchers applied the principles of population genetics such as mutation, genetic drift, migration, adaptation, and speciation 8 . These methodologies utilise genetic material (genetic markers) common across groups of individuals to define populations for provenance testing or to define species for species identification 8 . ...
... To develop timber tracking tools suitable for these species, researchers applied the principles of population genetics such as mutation, genetic drift, migration, adaptation, and speciation 8 . These methodologies utilise genetic material (genetic markers) common across groups of individuals to define populations for provenance testing or to define species for species identification 8 . During forensic timber identification, enforcement officers need to identify unknown samples at genus or species level correctly from the start, before further investigating geographic origin or individual identification. ...
International timber trade communities are increasingly demanding that timber in the wood supply chain be sourced from sustainably harvested forests and certified plantations. This is to combat illegal logging activities to prevent further depletion of our precious forests worldwide. Hence, timber tracking tools are important to support law enforcement officials in ensuring only sustainably harvested timbers are traded in the market. In this study, we developed chloroplast DNA (cpDNA) and simple sequence repeat (SSR) databases as tracking tools for an important tropical timber tree species, Shorealeprosula from Peninsular Malaysia. A total of 1410 individual trees were sampled from 44 natural populations throughout Peninsular Malaysia. Four cpDNA regions were used to generate a cpDNA haplotype database, resulting in a haplotype map comprising 22 unique haplotypes derived from 28 informative intraspecific variable sites. This cpDNA database can be used to trace the origin of an unknown log at the regional level. Ten SSR loci were used to develop the SSR allele frequency database. Bayesian cluster analysis divided the 44 populations into two genetic clusters corresponding to Region A and Region B. Based on conservativeness evaluation of the SSR databases for individual identification, the coancestry coefficients (θ) were adjusted to 0.1900 and 0.1500 for Region A and B, respectively. These databases are useful tools to complement existing timber tracking systems in ensuring only legally sourced timbers are allowed to enter the wood supply chain.
... Several institutional and international legal measures have been put in place to prevent overexploitation and irreversible loss of species and habitats [5][6][7]. Innovative programmes are emerging [8,9], solid research is under way [10][11][12][13][14], and research with significant impact and news items are being shared worldwide [15]. ...
... Machines can be easily misled by factors such as the source of images, which can be acquired in the field using mobile phones [90] or in a laboratory-controlled environment [71,114], and variables including different thicknesses, orientation, staining, digital artefacts and other variations, which is why many thin sections from historical wood collections are useful only to the trained human eye [10]. ...
Wood identification is an important tool in many areas, from biology to cultural heritage. In the fight against illegal logging, it has a more necessary and impactful application. Identifying a wood sample to genus or species level is difficult, expensive and time-consuming, even when using the most recent methods, resulting in a growing need for a readily accessible and field-applicable method for scientific wood identification. Providing fast results and ease of use, computer vision-based technology is an economically accessible option currently applied to meet the demand for automated wood identification. However, despite the promising characteristics and accurate results of this method, it remains a niche research area in wood sciences and is little known in other fields of application such as cultural heritage. To share the results and applicability of computer vision-based wood identification, this paper reviews the most frequently cited and relevant published research based on computer vision and machine learning techniques, aiming to facilitate and promote the use of this technology in research and encourage its application among end-users who need quick and reliable results.
... and Diospyros spp.) have been undertaken since 2014, and resulted in collection of new plant material in the field using a standardized sampling protocol that includes sampling of heartwood and herbarium voucher specimens, taxonomic investigations, and conservation assessments. In parallel, these resources have also been used to develop reference collections and databases for various forensic timber identification methods (reviewed in Dormontt et al. 2015 andSchmitz et al. 2020). ...
... Most of the interpretations in such studies relate to the variance of wood anatomical features within and between particular taxa (Wheeler et al. 2020). It is therefore important that the investigated specimens be fully documented (including high-quality herbarium vouchers deposited in one or several herbaria, with precise indication of the locality of origin) and confidently identified to species level by expert taxonomists (Schmitz et al. 2020). Even though the set of analyzed features was highly overlapping, we could only compare our results to four out of nine overlapping species documented in the InsideWood database, because the collections on which InsideWood is based were revealed to constitute a mixture of different species in two cases, an entirely different species in one case, while the species identity could not be fully verified in two further cases. ...
Rosewood and palisander (Dalbergia L.f., Fabaceae) are sources of highly valuable tropical timber and include species threatened by habitat degradation and selective logging for national and international trade. Law enforcement depends on reliable and cost-effective species-level identification of timber along the supply chain. The potential of wood anatomy to distinguish between species has not yet been systematically investigated for Dalbergia species from Madagascar. We assessed 36 qualitative and eight quantitative wood anatomical features in 16 Malagasy Dalbergia species that form medium-sized to large trees, representing each species by at least five individuals. We integrated and contrasted the newly collected data with existing data from InsideWood and two previous studies. Principal component analysis of 93 individuals and 29 variables resulted in non-overlapping hulls for eight species with respect to the first two dimensions. Four quantitative features (number of ray tiers per millimetre, number of rays per millimetre, vessel density, and vessel element length) and two qualitative features (scanty paratracheal axial parenchyma and irregular to absent storied structure) were found to be potentially diagnostic to distinguish three single species and three pairs of closely related species. Following our analyses, we provide a provisional microscopic wood anatomical identification key for the 16 Dalbergia species, which can be applied to both logs and sawn wood.
... To eliminate the risk of pathogenic fungi entering the United Kingdom, samples were subjected to 121 • C heat at 15 psi in an autoclave for 30 min before they were dried and released into the WFID collection for analysis and storage. Prior to routine preparation mold was manually removed as it is considered that it may be source of variability for stable isotope analysis (Horacek et al., 2018;Beeckman et al., 2020). ...
... Samples that presented with hyphae upon receipt at Kew had any mold physically removed as part of preparation in accordance with advice from Beeckman et al. (2020). Samples were dried at 103 • C before being coarsely ground and placed into a ballmill (Retsch MM220, Haan, Germany). ...
Consumers are becoming increasingly aware of the environmental impacts caused by deforestation and illegal logging and there is an increasing demand for supply chain transparency and traceability of wood products. Many importing and exporting nations have implemented regulations which aim to control the origin and species of traded timbers of high ecological importance and economic value. However, despite growing interest in method development for timber authentication purposes, many studies have been limited by insufficient numbers of authentic timber reference samples. Our aim was to address the differences in stable isotope ratio profile of bulk, homogenized wood samples collected from living or recently felled trees in two FSC concessions in Gabon, which are approximately 240 km apart, for the purposes of origin classification and protecting valuable forest commodities. Forty-seven timber samples comprising 10 genera of tropical trees were obtained using a Pickering Punch sampling device or chainsaw from two forest concessions in Gabon (Precious Woods Group and Compagnie des Bois du Gabon) during July 2019. Samples were subject to δ ¹⁸ O, δ ² H, δ ¹³ C, δ ¹⁵ N, and δ ³⁴ S stable isotope analysis using elemental analysis-isotope ratio mass spectrometry (EA-IRMS). Results show that significant differences are evident in the stable isotope ratios of Aucoumea klaineana between Precious Woods Group and Compagnie des Bois du Gabon forest concessions. Relationships are evident between climatic and geological variables and the stable isotope ratios of the samples suggesting that further degrees of origin classification may be achievable in Gabon. For other species, insufficient numbers meant the possibility to determine discriminating factors between the two concessions was limited though data from these samples may prove useful to contribute to the understanding of stable isotope variability in tropical timber. The data presented establish a basis for evaluating origin claims of forest products and timber from the Compagnie des Bois du Gabon and Precious Woods Group concessions and lay a foundation for future development of timber tracking technologies in Gabon. The technique can be used for purposes of due diligence or forensic investigation by law enforcement as part of demand-side regulations such as the EU Timber Regulation, Illegal Logging Prevention Act, or the Lacey Act.
... In the past two decades, various approaches, including chromatography (Papapetros et al., 2018;Zhao et al., 2021), mass spectrometry (MS) (Hori et al., 2016;Zhao et al., 2021), and DNA barcoding (CBOL Plant Working Group, 2009;Dong et al., 2015;Li et al., 2011;Manzanilla et al., 2022), have been used for species identification and geographic traceability. Among them, molecularbased methods have attracted much attention because of their significant advantages in accuracy, sensitivity, and high reproducibility (Dormontt et al., 2015;Fanelli et al., 2021;Lowe & Cross, 2011;Schmitz et al., 2020), and have been increasingly used for authenticity and traceability of food with plant or animal origin, such as lentil (Lens culinaris Medic.; Bosmali et al., 2012) and European lobster (Homarus gammarus L.; Jenkins et al., 2019), and for forensic identification of illegally traded species or biological products (Blanc-Jolivet et al., 2018;Hu et al., 2021;Wasser et al., 2004Wasser et al., , 2018. ...
Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA‐Seq based SNP markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a Tertiary relict restricted to four mountain regions in subtropical China. A total of 69 individuals from five populations (DLS, SHS, HP, BMS, and DYS) covering the entire range were used for transcriptome sequencing. Based on these transcriptomic data, we evaluated genetic variation and population structure of C. argyrophylla, and found extremely low nucleotide diversity but strong population differentiation. We also screened 113 population‐specific SNP loci, including 96 for BMS, 8 for DYS, 6 for SHS, 2 for HP, and 1 for one of the three subpopulations from DLS. According to these geographically diagnostic SNPs, we designed four population‐specific molecular barcodes for PCR amplification. To test the utility and efficiency of the four markers in geographic discrimination, double‐blind experiment was performed using 157 individuals labelled without any locality information. We found that almost all tested individuals could be successfully assigned to their geographic localities. Our work not only sheds some new light on the genetic profile of C. argyrophylla, but also provides a practical and cost‐efficient solution for geographic traceability using transcriptome‐derived SNPs.
... Any samples that were affected by hyphae had the mould removed prior to preparation in accordance with advice in Horacek et al. (2018) and Beeckman et al. (2020). Samples were initially dried at 103 • C before grinding/drilling. ...
Global demand for low-cost forest products is leading manufacturers and traders to
source timber and wood products from vulnerable nations and delicate ecosystems.
One small island nation, the Solomon Islands, is seeing exploitation of natural resources
accelerating to such a point that its natural forests may be exhausted by 2036. The
main causes of natural forest loss on the archipelago are unsustainable or illegal logging
practices. Various laws in consumer countries require that members of industry ensure
that only legally sourced timber is placed onto their respective national markets. Those
that break these laws or fail to act in a way that is compliant may be subject to
harsh penalties. This study aims to establish scientific data to evaluate claims that
timber has originated from the Solomon Islands. This will enable Operators to carry out
due diligence analysis and permit members of Law Enforcement to conduct forensic
investigations. Eighty timber core samples comprising 13 different genera of tropical
trees were obtained from mature trees in two sites in the Solomon Islands (Guadalcanal
and Kolombangara islands) during the period August 2019 to November 2019 using a
Pickering Punch sampling device. Homogenised core samples were subject to d18O,
d2H, d13C, and d34S stable isotope analysis using elemental analysis-isotope ratio mass
spectrometry. Additional stable isotope data from relevant taxa and geographic origins
(elevation, geographic co-ordinates) were also included in this research as an initial
assessment of differences in stable isotope ratios between countries. Results show
that significant differences are evident in the stable isotope ratios of the sampled taxa
within the Solomon Islands (Guadalcanal and Kolombangara Islands) and between other
countries. These data can be used as a basis of evaluation to evaluate origin claims of
timber or wood products from the Solomon Islands, particularly Kolombangara Island.
Furthermore, in the right context, these data can also be used to establish whether
timber or wood products declared to be from origins other than the Solomon Islands
have stable isotope ratios that are consistent with data from the Solomon Islands. If
not, this would suggest foreign timber/forest products are from elsewhere and are being
passed-off as originating from the Solomon Islands.
Understanding the macroscopic structure of wood and its formation is essential to identifying wood and evaluating its properties and quality. Depending on genetic background, environmental conditions, and tree developmental stage, the macroscopic structure of wood can vary greatly and produce specific macroscopic signatures. Here, a comprehensive outline of the wood’s macroscopic structure and the features that can be used to identify wood by macroscopic examination is presented. The planes of observations are first depicted, and the fundamental differences between softwoods and hardwoods are outlined. Then, all the different cell characteristics, arrangements, and distributions that can be macroscopically observed are illustrated with their influence on wood figure and texture and non-anatomical features.
Various problems worldwide are caused by illegal production and distribution of timber, such as deception about timber species and origin and illegal logging. Numerous studies on wood tracking are being conducted around the world to demonstrate the legitimacy of timber. Tree species identification is the most basic element of wood tracking research because the quality of wood varies greatly from species to species and is consistent with the botanical origin of commercially distributed wood. Although many recent studies have combined machine learning-based classification methods with various analytical methods to identify tree species, it is unclear which classification model is most effective. The purpose of this work is to examine and compare the performance of three supervised machine learning classification models, support vector machine (SVM), random forest (RF), and artificial neural network (ANN), in identifying five conifer species and propose an optimal model. Using direct analysis in real-time ionization combined with time-of-flight mass spectrometry (DART-TOF-MS), metabolic fingerprints of 250 individual specimens representing five species were collected three times. When the machine learning models were applied to classify the wood species, ANN outperformed SVM and RF. All three models showed 100% prediction accuracy for genus classification. For species classification, the ANN model had the highest prediction accuracy of 98.22%. The RF model had an accuracy of 94.22%, and the SVM had the lowest accuracy of 92.89%. These findings demonstrate the practicality of authenticating wood species by combining DART-TOF-MS with machine learning, and they indicate that ANN is the best model for wood species identification.
The highly valuable timber species Dalbergia cochinchinensis is severely threatened due to habitat loss and illegal logging throughout its distribution in mainland Southeast Asia and is listed on CITES Appendix II. This study proposes a strategy for conservation and sustainable management of the species based on assessment of genetic structure within and among natural populations. We developed SNP markers from RAD sequencing and used these in combination with SSR genotypes from a previous study to assess the genetic diversity in 26 populations of D. cochinchinensis across its entire range in Laos, Thailand, Cambodia and Vietnam. The species is able of clonal reproduction and we found that trees closer than 45 meters from each other can be clones. Genetic diversity and clustering analysis showed a clear division of populations into five geographical groups with differing levels of diversity. Assignment tests correctly identified the region of origin for approximately 90% of the samples, which demonstrates that despite a low number of successfully identified SNPs, the SSR + SNP marker panel has the potential for tracking the geographic origin of D. cochinchinensis timber for use in CITES regulation and enforcement. We propose the five identified groups to be considered as Management Units and that conservation and breeding programs should be based on a network of in situ and ex situ conservation stands representing the genetic variation among and within these units. We recommend that conservation efforts are directed towards community owned and managed lands, as this has proven an effective strategy locally.
Using chemical fingerprints for timber species identification is a relatively new, but promising technique. However, little is known about the effect of pre-processing spectral data parameter settings on the timber species classification accuracy. Therefore, this study presents an extensive and automated analysis method using the random forest machine learning algorithm on a set of highly valuable timber species from the Meliaceae family. Metabolome profiles were collected using direct analysis in real-time (DART™) ionisation coupled with time-of-flight mass spectrometry (TOFMS) analysis of heartwood specimens for 175 individuals (representing 10 species). In order to analyse variability in classification accuracy, 110 sets of data pre-processing parameter combinations consisting of mass tolerance for binning and relative abundance cut-off thresholds were tested. Furthermore, for each set of parameters (designated “binning/threshold setting”), a random search for one hyperparameter of interest was performed, i.e. the number of variables (in this case ions) drawn randomly for each random forest analysis. The best classification accuracy (82.2%) was achieved with 47 variables and a binning and threshold combination of 40 mDa and 4%, respectively. Entandrophragma angolense is mostly confused with Entandrophragma candollei and Khaya anthotheca, and several Swietenia species are confused with each other due to the high similarity of their chemical fingerprints. Entandrophragma cylindricum, Entandrophragma utile, Khaya ivorensis, Lovoa trichilioides and Swietenia macrophylla are easy to discriminate and show less misclassifications. The choice of parameter settings, whether it is in the data pre-processing (binning and threshold) or classification algorithm (hyperparameters), results in variability in classification accuracy. Therefore, a preliminary parameter screening is proposed before constructing the final model when using the random forest algorithm for classification. Overall, DART-TOFMS in combination with random forest is a powerful tool for species identification.
• We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.
• We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.
• Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).
• Despite large heterogeneities caused by genus‐specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species‐rich tropical forests.
We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed.
There are nearly 40 items that should ideally be reported when an NIR (near infrared) spectroscopy project is completed, either as a report or as a scientific paper. However, in our reading of the extensive literature, many of the papers presented or published report no more than 6–10 of these. The purpose of this tutorial is to indicate all of the items and the reasons for reporting them. Most of the items that need to be reported are important for anyone who seeks to duplicate the type of application and methods reported in a peer-reviewed journal article for their own work. Practically, all of the items are significant to any worker if the eventual objective of their work is to extend it to the level of industrial application. The tutorial will summarize these items, and give some explanation for their inclusion. The tutorial should be useful to potential authors, as well as to reviewers.
Confronted with growing competition, wood industry manufacturers are increasingly looking to optimize their processing processes and to control the quality of their finished products. Similarly, research and development teams in genetics and forest genetic improvement need new powerful tools enabling the evaluation of a large number of samples at a low cost and quickly. In this context, the development of non-destructive tools for measuring wood material performances (in all its forms: massive, de structured or reconstructed) is essential. Since the early 1990s, numerous research studies have explored the usefulness of using Near Infrared Spectroscopy (NIRS) to estimate the properties of wood material.This chapter, divided into two parts, aims to present a state of the art on the use of NIRS methodology in the wood domain. The first part describes technology and principles of its operation as well as its various fields of application for macromolecules, some physical and mechanical properties. The second part takes stock of the latest knowledge gained to date on the use of NIRS in the cooperage sector and takes example of an original industrial process for measuring the quality of oak wood directly on the production line.
Dipteryx timber has been heavily exploited in South America since 2000's due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to six different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy-Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial SNPs, and two chloroplast and five mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in D. odorata and D. ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbour approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber.
We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.